Biology Projects

Nitrogenase Directed Evolution

One of our active projects is the directed evolution of a thermophilic nitrogenase. Nitrogenase enzymes convert N2 to ammonia but are usually poisoned by O2, making the enzyme useless in many environments. Plants have overcome the O2-poisoning barrier by creating complex structures to block O2 diffusion. Engineering such a structure in plants that don't already have it has challenged scientists for years. While a nitrogenase from the thermophilic species Streptomyces thermoautotrophicus has been shown to work in the presence of O2, it only operates efficiently at 65C. Our goal is to make a nitrogenase enzyme that works at 23C and is not poisoned by O2. Such an enzyme could be useful in many industrial settings. We are doing this by using a process called "directed evolution." Read More on the Wiki

EGCG and Telomeres

Sophia and crew are exploring the possible connection between the compound epigallocatechin gallate (EGCG) and telomere maintenance. EGCG is an antioxidant found in great abundance in green tea. Given green tea's common use in treating cancer and aging, she thought EGCG might be involved in telomere maintenance. To study this, she is using the Tetrahymena thermophila, a ciliated protozoan that is perfect for telomere research due to it's hundreds of chromosomes (more telomeres per cell) and it's ease of handling. Initial experiments involved using qPCR to quantify telomere lengths in samples treated with varying concentrations of EGCG. Those dose response curves showed a shortening of telomeres in response to higher concentrations. To follow up on these results, she has been developing a technique to quantify telomeres using FISH staining in fixed T thermophila. More data to come...

GFP E. coli

It's E. coli and it glows! This project is our proof of concept showing that we have all the equipment, reagents, and know-how necessary to create recombinant DNA and genetically modify bacteria. Aside from being a proof of concept, it also serves as a crash course in molecular biology for those that haven't done such techniques before. The whole thing can (almost) be completed in a single day. The project starts off by PCR-ing the gene for green fluorescent protein, a 238 amino acid protein that absorbs blue light and emits green, from a basic cloning plasmid. The fragment is purified using a standard silica-based column and then cut with the EcoRI restriction enzyme. The restriction causes the ends of the fragment to have overhangs which are compatible with the target plasmid's overhangs. The GFP fragment is then ligated into the pMAL-pIII plasmid. The plasmid is then transformed into E. coli and grown on LB media plus antibiotics to select for transformed bacteria. The end result is a bunch of E. coli colonies that glow green under blue or UV light. This project is fun and teaches basic molecular biology, sterile technique and basic liquid handling. Plus, you get green glowing bacteria! Read More on the Wiki


We have picked up an Emotiv Epoc and are running it in combination with the EmoKit python module. Our plans for it include biofeedback, brain-computer interface for EverQuest and reverse engineering for a more efficient / open design. Read more on the wiki


An Amazon cloud-based pipeline for microarray expression data analysis. Proof of concept will involve the entirety of GEO's human expression chips. Read More on the Wiki


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